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Dynemicin A has the ability to undergo the Bergman cyclization, forming a para-benzyne moiety with the ability to induce DNA strand scission. This property of dynemicin A makes it a promising anti-tumor agent. Past research has shown conclusively that dynemicin A binds to and abstracts a hydrogen atom (H5') from the DNA backbone, but the molecular mechanism of the binding event is not fully understood. We have used AMBER Molecular Dynamics simulations to investigate the dynamics associated with the reaction mechanisms. Previously, two binding mechanisms have been proposed, of which the second is more supported: (1) dynemicin A intercalates between two base pairs and directly abstracts a hydrogen atom from DNA and (2) dynemicin A inserts into the minor groove and directly abstracts a hydrogen atom from DNA. We propose a third mechanism, where dynemicin A intercalates, then undergoes a proximate, intramolecular hydrogen atom abstraction (internal abstraction). While not studied here, the resulting radical would then subsequently abstract a hydrogen atom from DNA.

Original publication





Journal of molecular graphics & modelling

Publication Date





251 - 264


Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, 28 Westhampton Way, Richmond, VA 23173, United States.


Anthraquinones, DNA, Intercalating Agents, Binding Sites, Base Sequence, Nucleic Acid Conformation, Base Pairing, Hydrogen Bonding, Thermodynamics, Enediynes, Molecular Dynamics Simulation